Description

Maps Hi-C reads in unaligned CRAM format to a set of references.

Input

Name
Description
Pattern

ch_assemblies (file)

Input channel containing assemblies to align Hi-C reads to Structure: [ val(meta), path(fasta) ]

*.fn?a(sta)?(.gz)?

ch_hic_cram (file)

Input channel containing Hi-C CRAM files for mapping. Structure: [ val(meta), path(cram) ] or [ val(meta), [ path(cram1), path(cram2), ... ] ]

*.cram

val_aligner (string)

Which aligner to use - bwamem2 or minimap2

val_cram_chunk_size (integer)

Size of chunk to split CRAM files into

val_mark_duplicates (boolean)

Whether to mark duplicates on the merged BAM or not

Output

Name
Description
Pattern

bam (file)

Channel containing the BAM files describing Hi-C alignments to the input assemblies Structure: [ val(meta), path(bam) ]

*.bam

bam_index (file)

Channel containing the indexes for the output BAM Structure: [ val(meta), path(bam) ]

*.{bai,csi,crai}

Components

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